Class ExtractSequences


  • @DocumentedFeature
    public class ExtractSequences
    extends CommandLineProgram
    Simple command line program that allows sub-sequences represented by an interval list to be extracted from a reference sequence file.
    • Field Detail

      • INTERVAL_LIST

        @Argument(doc="Interval list describing intervals to be extracted from the reference sequence.")
        public File INTERVAL_LIST
      • OUTPUT

        @Argument(shortName="O",
                  doc="Output FASTA file.")
        public File OUTPUT
      • LINE_LENGTH

        @Argument(doc="Maximum line length for sequence data.")
        public int LINE_LENGTH
    • Constructor Detail

      • ExtractSequences

        public ExtractSequences()
    • Method Detail

      • doWork

        protected int doWork()
        Description copied from class: CommandLineProgram
        Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
        Specified by:
        doWork in class CommandLineProgram
        Returns:
        program exit status.